[gmx-users] (no subject)
mark.j.abraham at gmail.com
Sat Nov 19 21:36:38 CET 2016
No, the warning is general... "If there are..." mdrun does not attempt to
write the trajectory that you think you want for analysis ;-) There's an
infinite number of equivalent representations, and you need to think (and
invoke trjconv) to get the one that you want.
On Sat, Nov 19, 2016 at 8:38 PM tasneem kausar <tasneemkausar12 at gmail.com>
> Dear Kingsley
> You are directly calculating the rms after combining the xtc file. It is
> clear from the warning that you did not apply perodic boundary condition on
> you trajectory.
> Try trjconv -f combined.xtc -s refrence.tpr -o combined_pbc.xtc -pbc whole
> -center command after trjcat. After trjconv calculate RMS.
> On Sat, Nov 19, 2016 at 11:06 AM, Kingsley Theras Primus Dass . <
> 105726107 at gms.tcu.edu.tw> wrote:
> > Dear Users!!
> > I have a question about RMSD. I ran MＤ simulaton for 500ns and
> > all my .xtc files using trjcat command.
> > And , then I used g_rms command with the connected .xtc file to calculate
> > RMSD for backbone atoms. But , when I run g_rms command , I get a warning
> > as follows:
> > WARNING: If there are molecules in the input trajectory file
> > that are broken across periodic boundaries, they
> > cannot be made whole (or treated as whole) without
> > you providing a run input file.
> > Can someone say , why this warning msg is coming, and how should i need
> > avoid this. what measure should i need to take ?
> > Thank you.
> > --
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